Well, nobody ever asked that question before. Surprisingly, to me at least, there are API calls to get and set Application variables Here is some help on that.
https://helpv2.quickbase.com/hc/en-us/articles/4418302337428-API-GetDBVar
An alternative using Application Variables would be a helper table with only one record in it and setting a relationship from that one record to any other table where you need the values looked up. Or you could use a formula query.
Then you could edit that record more "normally" by editing that record.
An advantage of storing values on a regular Quickbase record is they become visible to users and you can have users manually edit who are not administrators.
You use a Make Request step to call the API.